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- PDB-9jp2: COMPLEX STRUCTURE OF ENDO-1,3-FUCANASE WITH FUCOTETRAOSE -

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Basic information

Entry
Database: PDB / ID: 9jp2
TitleCOMPLEX STRUCTURE OF ENDO-1,3-FUCANASE WITH FUCOTETRAOSE
ComponentsGlycoside-hydrolase family GH114 TIM-barrel domain-containing protein
KeywordsHYDROLASE / Endo-1.3-fucanase / GH168
Function / homologyHypothetical glycosyl hydrolase family 15 / Hypothetical glycosyl hydrolase family 15 / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein
Function and homology information
Biological speciesNovipirellula artificiosorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsChen, G.N. / Chang, Y.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U22A20542 China
CitationJournal: To Be Published
Title: Complex structure of endo-1.3-fucanase with fucotetraose at 2.02 Angstroms resulution.
Authors: Chen, G.N. / Chang, Y.G.
History
DepositionSep 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6902
Polymers46,7671
Non-polymers9231
Water4,864270
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.360, 148.360, 42.028
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein


Mass: 46766.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novipirellula artificiosorum (bacteria)
Gene: Poly41_55130 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5C6D8T6
#2: Polysaccharide alpha-L-fucopyranose-(1-3)-2,4-di-O-sulfo-alpha-L-fucopyranose-(1-3)-2-O-sulfo-alpha-L-fucopyranose- ...alpha-L-fucopyranose-(1-3)-2,4-di-O-sulfo-alpha-L-fucopyranose-(1-3)-2-O-sulfo-alpha-L-fucopyranose-(1-3)-2-O-sulfo-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 922.833 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
[][a-L-Fucp2SO3]{[(3+1)][a-L-Fucp2SO3]{[(3+1)][a-L-Fucp2SO34SO3]{[(3+1)][a-L-Fucp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.03 M Citric acid, 0.07 M BIS-TRIS propane / pH 7.6, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.02→42.83 Å / Num. obs: 20953 / % possible obs: 92 % / Redundancy: 9.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.043 / Rrim(I) all: 0.134 / Χ2: 0.97 / Net I/σ(I): 13.6 / Num. measured all: 199565
Reflection shellResolution: 2.02→2.12 Å / % possible obs: 67.7 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.93 / Num. measured all: 20423 / Num. unique obs: 2254 / CC1/2: 0.767 / Rpim(I) all: 0.323 / Rrim(I) all: 0.986 / Χ2: 0.87 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→42.83 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2171 1994 9.52 %
Rwork0.1695 --
obs0.174 20952 91.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→42.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2872 0 57 270 3199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073026
X-RAY DIFFRACTIONf_angle_d0.9384109
X-RAY DIFFRACTIONf_dihedral_angle_d7.65390
X-RAY DIFFRACTIONf_chiral_restr0.052427
X-RAY DIFFRACTIONf_plane_restr0.008518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.040.3047870.2615820X-RAY DIFFRACTION100
2.08-2.120.27531220.20971171X-RAY DIFFRACTION100
2.12-2.180.2841570.21211459X-RAY DIFFRACTION100
2.18-2.220.2533890.2018827X-RAY DIFFRACTION100
2.26-2.330.24751530.20511428X-RAY DIFFRACTION100
2.34-2.430.25321560.18521460X-RAY DIFFRACTION100
2.43-2.540.25471530.20511458X-RAY DIFFRACTION100
2.54-2.670.30751530.19421481X-RAY DIFFRACTION100
2.67-2.840.23021550.19631498X-RAY DIFFRACTION100
2.84-3.060.22091470.1771453X-RAY DIFFRACTION100
3.06-3.370.22341520.17781484X-RAY DIFFRACTION100
3.37-3.850.21221560.14131473X-RAY DIFFRACTION100
3.86-4.860.17811570.13331481X-RAY DIFFRACTION100
4.86-42.830.15541570.15181465X-RAY DIFFRACTION100

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